This directory contains compressed multiple alignments of the 
following assemblies to the human genome (hg17, May 2004):

  - chimp (Nov 2003, panTro1)
  - macaque (Jan 2006, rheMac2)
  - mouse (May 2004, mm7)
  - rat (Jun 2003, rn3)
  - rabbit (May 2005, oryCun1)
  - dog (May 2005, canFam2)
  - cow (Mar 2005, bosTau2)
  - armadillo (May 2005, dasNov1)
  - elephant (May 2005, loxAfr1)
  - tenrec (Jul 2005, echTel1)
  - opossum (Jun 2005, monDom2)
  - chicken (Feb 2004, galGal2)
  - frog (Oct 2004, xenTro1)
  - zebrafish (May 2005, danRer3)
  - Tetraodon (Feb 2004, tetNig1)
  - Fugu (Aug 2002, fr1) 

The chr*.maf.gz files each contain all the alignments to that 
particular human chromosome.

The maf/upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for RefSeq genes with annotated 5' UTRs.
These files differ from the standard MAF format: they display
alignments that extend from start to end of the upstream region in 
human, whether or not alignments actually exist. In situations where no  
alignments exist or the alignments of one or more species are missing, 
dot (".") is used as a placeholder. Multiple regions of an assembly's
sequence may align to a single region in human; therefore, only the 
species name is displayed in the alignment data and no position information 
is recorded. The alignment score is always zero in these files. These files
are updated weekly.

For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.

---------------------------------------------------------------
If you plan to download a large file or multiple files from this 
directory, we recommend that you use ftp rather than downloading the 
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, 
then go to the directory goldenPath/hg17/multiz17way. To download 
multiple files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

All the files in this directory are freely usable for any 
purpose. For data use restrictions regarding the individual 
genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.

      Name                    Last modified      Size  Description
Parent Directory - maf/ 2019-11-06 11:00 - 17way.nh 2006-09-18 09:21 588 md5sum.txt 2008-10-16 12:26 2.2K chr18_random.maf.gz 2006-04-13 15:27 23K chrM.maf.gz 2006-04-13 16:04 95K chr16_random.maf.gz 2006-04-13 15:24 145K chr10_random.maf.gz 2006-04-13 15:10 188K chr5_random.maf.gz 2006-04-13 15:50 202K chr6_hla_hap1.maf.gz 2006-04-13 15:54 285K chr6_hla_hap2.maf.gz 2006-04-13 15:54 298K chr19_random.maf.gz 2006-04-13 15:28 359K chr13_random.maf.gz 2006-04-13 15:18 457K chr2_random.maf.gz 2006-04-13 15:37 482K chr22_random.maf.gz 2006-04-13 15:37 512K chr8_random.maf.gz 2006-04-13 16:01 821K chr12_random.maf.gz 2006-04-13 15:16 920K chr7_random.maf.gz 2006-04-13 15:57 958K chr9_random.maf.gz 2006-04-13 16:04 1.0M chr4_random.maf.gz 2006-04-13 15:46 1.3M chr15_random.maf.gz 2006-04-13 15:22 1.6M chr3_random.maf.gz 2006-04-13 15:42 1.8M chrX_random.maf.gz 2006-04-13 16:06 1.9M chr17_random.maf.gz 2006-04-13 15:26 3.2M chr6_random.maf.gz 2006-04-13 15:54 3.5M chr1_random.maf.gz 2006-04-13 15:28 6.9M chrY.maf.gz 2006-04-13 16:07 28M chr21.maf.gz 2006-04-13 15:36 71M chr22.maf.gz 2006-04-13 15:37 72M chr19.maf.gz 2006-04-13 15:28 103M chr20.maf.gz 2006-04-13 15:36 133M chr18.maf.gz 2006-04-13 15:27 166M chr16.maf.gz 2006-04-13 15:24 177M chr17.maf.gz 2006-04-13 15:26 178M chr15.maf.gz 2006-04-13 15:22 190M chr14.maf.gz 2006-04-13 15:20 198M chr13.maf.gz 2006-04-13 15:18 207M chr9.maf.gz 2006-04-13 16:04 262M chrX.maf.gz 2006-04-13 16:06 264M chr12.maf.gz 2006-04-13 15:16 286M chr11.maf.gz 2006-04-13 15:13 297M chr10.maf.gz 2006-04-13 15:10 298M chr8.maf.gz 2006-04-13 16:01 308M chr7.maf.gz 2006-04-13 15:57 334M chr6.maf.gz 2006-04-13 15:54 376M chr5.maf.gz 2006-04-13 15:50 397M chr4.maf.gz 2006-04-13 15:46 401M chr3.maf.gz 2006-04-13 15:42 446M chr1.maf.gz 2006-04-13 15:07 511M chr2.maf.gz 2006-04-13 15:34 540M